fix airlock

MaastrichtU-IDS · Apr 11, 2024 · 06d88bc · 06d88bc
1 parent 232723e
commit 06d88bc
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Showing 3 changed files with 9 additions and 33 deletions.
diff --git a/backend/src/upload.py b/backend/src/upload.py
@@ -185,7 +185,7 @@ def to_camelcase(s: str) -> str:
     s = sub(r"(_|-)+", " ", s).title().replace(" ", "")
     return "".join([s[0].lower(), s[1:]])
 
-def load_cohort_dict_file(dict_path: str, cohort_id: str, airlock: bool) -> Dataset:
+def load_cohort_dict_file(dict_path: str, cohort_id: str) -> Dataset:
     """Parse the cohort dictionary uploaded as excel or CSV spreadsheet, and load it to the triplestore"""
     # print(f"Loading dictionary {dict_path}")
     # df = pd.read_csv(dict_path) if dict_path.endswith(".csv") else pd.read_excel(dict_path)
@@ -219,8 +219,6 @@ def load_cohort_dict_file(dict_path: str, cohort_id: str, airlock: bool) -> Data
         g = init_graph()
         g.add((cohort_uri, RDF.type, ICARE.Cohort, cohort_uri))
         g.add((cohort_uri, DC.identifier, Literal(cohort_id), cohort_uri))
-        # Preview goes to mapping graph because it is defined in the explorer UI
-        g.add((cohort_uri, ICARE.previewEnabled, Literal(str(airlock).lower(), datatype=XSD.boolean), get_cohort_mapping_uri(cohort_id)))
 
         # Record all errors and raise them at the end
         errors = []
@@ -358,7 +356,9 @@ async def upload_cohort(
         shutil.copyfileobj(cohort_dictionary.file, buffer)
 
     try:
-        g = load_cohort_dict_file(metadata_path, cohort_id, airlock)
+        g = load_cohort_dict_file(metadata_path, cohort_id)
+        # Airlock preview setting goes to mapping graph because it is defined in the explorer UI
+        g.add((get_cohort_uri(cohort_id), ICARE.previewEnabled, Literal(str(airlock).lower(), datatype=XSD.boolean), get_cohort_mapping_uri(cohort_id)))
         # Delete previous graph for this file from triplestore
         delete_existing_triples(get_cohort_uri(cohort_id))
         publish_graph_to_endpoint(g)
@@ -467,7 +467,7 @@ def init_triplestore() -> None:
             for file in glob.glob(os.path.join(folder_path, "*_datadictionary.*")):
                 # NOTE: default airlock preview to false if we ever need to reset cohorts,
                 # admins can easily ddl and reupload the cohorts with the correct airlock value
-                g = load_cohort_dict_file(file, folder, False)
+                g = load_cohort_dict_file(file, folder)
                 g.serialize(f"{settings.data_folder}/cohort_explorer_triplestore.trig", format="trig")
                 if publish_graph_to_endpoint(g):
                     print(f"💾 Triplestore initialization: added {len(g)} triples for cohorts {file}.")

diff --git a/frontend/src/components/CohortsContext.tsx b/frontend/src/components/CohortsContext.tsx
@@ -15,19 +15,6 @@ export const CohortsProvider = ({children}: any) => {
   const [userEmail, setUserEmail]: [string | null, any] = useState('');
   const worker: MutableRefObject<Worker | null> = useRef(null);
 
-  // Update cohorts data with a web worker in the background for smoothness
-  // const worker = new Worker('/cohortsWorker.js');
-  // worker.onmessage = (event) => {
-  //   // Update your state with the new data
-  //   const data = event.data;
-  //   if (!data.error) {
-  //     setCohortsData(data);
-  //     console.log('Updated context with data', data);
-  //   } else {
-  //     console.error('Error fetching data in worker:', data.error);
-  //   }
-  // };
-
   useEffect(() => {
     setDataCleanRoom(JSON.parse(sessionStorage.getItem('dataCleanRoom') || '{"cohorts": {}}'));
 
@@ -61,6 +48,7 @@ export const CohortsProvider = ({children}: any) => {
   // Fetch cohorts data from the API using the web worker
   const fetchCohortsData = () => {
     worker.current?.postMessage({apiUrl});
+    // console.log(cohortsData)
   };
 
   // Update the metadata of a specific cohort in the context

diff --git a/frontend/src/components/Nav.tsx b/frontend/src/components/Nav.tsx
@@ -36,11 +36,8 @@ export function Nav() {
 
   const toggleTheme = () => {
     const newTheme = theme === 'light' ? 'dark' : 'light';
-    // console.log("NEW THEME", newTheme)
     sessionStorage.setItem('theme', newTheme);
     setTheme(newTheme);
-    // document.querySelector('html')?.setAttribute('data-theme', newTheme);
-    // document.documentElement.setAttribute("data-theme", newTheme);
   };
 
   const handleLogout = () => {
@@ -63,27 +60,18 @@ export function Nav() {
   const sendCohortsToDecentriq = async () => {
     setIsLoading(true);
     // Replace with actual API endpoint and required request format
-    console.log('Sending request to Decentriq', dataCleanRoom);
-    const requestBody = dataCleanRoom;
-    // const requestBody = {cohorts: {}};
-    // for (const cohortId of dataCleanRoom.cohorts as string[]) {
-    //   // @ts-ignore
-    //   // requestBody.cohorts[cohortId] = cohortsData[cohortId];
-    //   // NOTE: variables is left empty for now, placeholder for later when users will be able to select also variables
-    //   requestBody.cohorts[cohortId] = {"variables": []};
-    // }
-    console.log('requestBody', requestBody);
+    // console.log('Sending request to Decentriq', dataCleanRoom);
     try {
       const response = await fetch(`${apiUrl}/create-dcr`, {
         method: 'POST',
         credentials: 'include',
         headers: {
           'Content-Type': 'application/json'
         },
-        body: JSON.stringify(requestBody)
+        body: JSON.stringify(dataCleanRoom)
       });
       const res = await response.json();
-      console.log(res);
+      // console.log(res);
       setPublishedDCR(res);
       setIsLoading(false);
       // Handle response